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K thanks for clarifying. I think I have a better understanding now of what's going on. I'm assuming you are finding the links that are pointing to your site through Webmaster Tools. It can take weeks after google has recrawled the page for your updated link profile to be reflected in GWT. But if you are going to theses websites with 404 pages and your link is no longer there then you should have nothing to worry about. I would suggest thoroughly reviewing the links on all the pages that are said to be linking to you and and view the source code for no display tags with links to your site. Unless you own or have permission from the website with the 404 pages, the Removal Tool won't allow you to remove the page from their index. Have you checked on any link explorers to see if they are displaying the same links? Maybe it will provide you with a more refreshed link profile.